3QAQ

Crystal structure of PI3K-gamma in complex with triazine-benzimidazole 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of triazine-benzimidazoles as selective inhibitors of mTOR.

Peterson, E.A.Andrews, P.S.Be, X.Boezio, A.A.Bush, T.L.Cheng, A.C.Coats, J.R.Colletti, A.E.Copeland, K.W.Dupont, M.Graceffa, R.Grubinska, B.Harmange, J.C.Kim, J.L.Mullady, E.L.Olivieri, P.Schenkel, L.B.Stanton, M.K.Teffera, Y.Whittington, D.A.Cai, T.La, D.S.

(2011) Bioorg.Med.Chem.Lett. 21: 2064-2070

  • DOI: 10.1016/j.bmcl.2011.02.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • mTOR is part of the PI3K/AKT pathway and is a central regulator of cell growth and survival. Since many cancers display mutations linked to the mTOR signaling pathway, mTOR has emerged as an important target for oncology therapy. Herein, we report th ...

    mTOR is part of the PI3K/AKT pathway and is a central regulator of cell growth and survival. Since many cancers display mutations linked to the mTOR signaling pathway, mTOR has emerged as an important target for oncology therapy. Herein, we report the discovery of triazine benzimidazole inhibitors that inhibit mTOR kinase activity with up to 200-fold selectivity over the structurally homologous kinase PI3Kα. When tested in a panel of cancer cell lines displaying various mutations, a selective inhibitor from this series inhibited cellular proliferation with a mean IC(50) of 0.41 μM. Lead compound 42 demonstrated up to 83% inhibition of mTOR substrate phosphorylation in a murine pharmacodynamic model.


    Organizational Affiliation

    Medicinal Chemistry, Amgen Inc, 360 Binney St, Cambridge, MA 02142, USA. epeterso@amgen.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
A
960Homo sapiensMutation(s): 0 
Gene Names: PIK3CG
EC: 2.7.1.153
Find proteins for P48736 (Homo sapiens)
Go to Gene View: PIK3CG
Go to UniProtKB:  P48736
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
QAQ
Query on QAQ

Download SDF File 
Download CCD File 
A
[(4-{2-[(3-hydroxyphenyl)amino]-1H-benzimidazol-1-yl}-1,3,5-triazin-2-yl)amino]acetonitrile
2-(4-(2-(3-hydroxyphenylamino)-1H-benzo[d]imidazol-1-yl)-1,3,5-triazin-2-ylamino)acetonitrile
C18 H14 N8 O
FEBJYEFFVIDUNF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QAQIC50: 100 nM (100) BINDINGDB
QAQKi: 120 nM (100) BINDINGDB
QAQIC50: 100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 145.395α = 90.00
b = 68.579β = 94.69
c = 106.501γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
ADSCdata collection
EPMRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance